On 01/12/2012 01:05 PM, Jim Robison-Cox wrote:
Hi,
I'm trying to install rjags and R2jags with R version 2.14.1 (2011-12-22)
on
Linux Mint 12 machine using
software repository:
deb http://cran.fhcrc.org/bin/linux/ubuntu oneiric/
jags seems to install OK, but rjags gives a weird error about not
finding fprec symbol.
Here is a history of the problem including several attempts to work
around it.
(Because of Ben Bolker's recent post, I first removed jags)
sudo apt-get remove jags
## The following packages will be REMOVED:
## jags r-cran-rjags
sudo apt-get install jags
## The following NEW packages will be installed:
## jags
## Unpacking jags (from .../jags_3.2.0-1oneiric0_amd64.deb)
sudo apt-get install r-cran-rjags
##The following NEW packages will be installed:
##r-cran-rjags
## Unpacking r-cran-rjags (from .../r-cran-rjags_3.3-1_amd64.deb)
sudo apt-get install r-cran-r2jags
## The following packages have unmet dependencies:
## r-cran-r2jags : Depends: r-cran-r2winbugs but it is not installable
##E: Unable to correct problems, you have held broken packages.
sudo apt-get install r-cran-r2winbugs
## Package r-cran-r2winbugs is not available, but is referred to by
another package.
wget http://cran.fhcrc.org/src/contrib/R2WinBUGS_2.1-18.tar.gz
sudo R CMD INSTALL R2WinBUGS_2.1-18.tar.gz
## * DONE (R2WinBUGS)
wget http://cran.fhcrc.org/src/contrib/R2jags_0.03-02.tar.gz
sudo R CMD INSTALL R2jags_0.03-02.tar.gz
##module basemod loaded
##Error : .onLoad failed in loadNamespace() for 'rjags', details:
## call: dyn.load(file)
## error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
## /usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
Start R with
sudo R
require(rjags)
Loading required package: rjags
linking to JAGS 3.2.0
module basemod loaded
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file)
error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
/usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
install.packages("R2WinBUGS")
* DONE (R2WinBUGS)
install.packages("R2jags")
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file)
error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
/usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
Error : package ‘rjags’ could not be loaded
install.packages("R2jags")
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.fhcrc.org/src/contrib/R2jags_0.03-02.tar.gz'
Content type 'application/x-gzip' length 25915 bytes (25 Kb)
opened URL
==================================================
downloaded 25 Kb
* installing *source* package ‘R2jags’ ...
** package ‘R2jags’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
module basemod loaded
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file)
error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
/usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
Error : package ‘rjags’ could not be loaded
ERROR: lazy loading failed for package ‘R2jags’
* removing ‘/usr/local/lib/R/site-library/R2jags’
q()
If I try installing the newer rjags3.5, I get this error:
sudo R CMD INSTALL rjags_3-5.tar.gz
#linking to JAGS 3.2.0
#module basemod loaded
#Error : .onLoad failed in loadNamespace() for 'rjags', details:
# call: dyn.load(file)
# error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
# /usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
#ERROR: installing package indices failed
#* removing ‘/usr/local/lib/R/site-library/rjags’
Jim,
I do not have Linux Mint available to test, but in a clean version of
Ubuntu 11.10, adding only the RRutter PPA
(https://launchpad.net/~marutter/+archive/rrutter for details), I am
able to install jags,r-cran-rjags, r-cran-r2jags, and r-cran-r2winbugs
without any issues and they run without any issues.
I should note that due to a slight change in the numbering on CRAN,
r-cran-rjags version 3.5 needs to be forced to be installed over the
r-cran-jags version 3.3 that is available in the Ubuntu universe
repositories.
Since you were unable to install r-cran-r2winbugs, I would make sure the
RRutter repository is enabled. Then everything should install and work
correctly. If it doesn't, my first guess is a difference between Mint
and Ubuntu, but I cannot check that out right now.
Michael
--
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter
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